From tony.travis at abdn.ac.uk Sun Sep 7 09:06:55 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Sun, 7 Sep 2014 14:06:55 +0100 Subject: [Bio-linux-dev] APT sources in BL 8.0.3 Message-ID: <540C586F.8000004@abdn.ac.uk> Hi, Tim. I've just done a clean install from your BL 8.0.3 .iso and had problems with some of the APT sources: I made some changes to get it to update, note the comments about automatically configured Google sources :-( HTH, Tony. > root at kitcat:/etc/apt/sources.list.d# > diff -Naur bio-linux-legacy.list.orig bio-linux-legacy.list > --- bio-linux-legacy.list.orig 2014-09-02 01:14:20.792528304 +0100 > +++ bio-linux-legacy.list 2014-09-07 00:24:49.924652803 +0100 > @@ -1,4 +1,5 @@ > # Bio-Linux legacy packages (manually built, there is no deb-src) > # But there is an alternative mirror you can use. > # deb http://distro.ibiblio.org/bio-linux/packages/ unstable bio-linux > -deb http://nebc.nerc.ac.uk/bio-linux/ trusty bio-linux > +#deb http://nebc.nerc.ac.uk/bio-linux/ trusty bio-linux > +deb http://nebc.nerc.ac.uk/bio-linux/ unstable bio-linux > > diff -Naur google-chrome.list.orig google-chrome.list > --- google-chrome.list.orig 2014-09-02 01:14:20.792528304 +0100 > +++ google-chrome.list 2014-09-07 00:36:53.396678979 +0100 > @@ -1,3 +1,4 @@ > ### THIS FILE IS AUTOMATICALLY CONFIGURED ### > # You may comment out this entry, but any other modifications may be lost. > -deb http://dl.google.com/linux/chrome/deb/ trusty main > +# deb http://dl.google.com/linux/chrome/deb/ trusty main > +deb http://dl.google.com/linux/chrome/deb/ stable main > > rdiff -Naur google-talkplugin.list google-talkplugin > --- google-talkplugin.list 2014-09-07 00:38:08.724681705 +0100 > +++ google-talkplugin 1970-01-01 01:00:00.000000000 +0100 > @@ -1,4 +0,0 @@ > -### THIS FILE IS AUTOMATICALLY CONFIGURED ### > -# You may comment out this entry, but any other modifications may be lost. > -#deb http://dl.google.com/linux/talkplugin/deb/ trusty main > -deb http://dl.google.com/linux/talkplugin/deb/ stable main -- Dr. A.J.Travis, University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. From tony.travis at abdn.ac.uk Sun Sep 7 09:17:31 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Sun, 7 Sep 2014 14:17:31 +0100 Subject: [Bio-linux-dev] APT sources in BL 8.0.3 In-Reply-To: <540C586F.8000004@abdn.ac.uk> References: <540C586F.8000004@abdn.ac.uk> Message-ID: <540C5AEB.6020609@abdn.ac.uk> On 07/09/14 14:06, Tony Travis wrote: > rdiff -Naur google-talkplugin.list google-talkplugin Hi, Tim. Sorry, bit of finger trouble there: > diff -Naur google-talkplugin.list.orig google-talkplugin.list [ 2:15PM] > --- google-talkplugin.list.orig 2014-09-02 01:14:20.792528304 +0100 > +++ google-talkplugin.list 2014-09-07 00:38:08.724681705 +0100 > @@ -1,3 +1,4 @@ > ### THIS FILE IS AUTOMATICALLY CONFIGURED ### > # You may comment out this entry, but any other modifications may be lost. > -deb http://dl.google.com/linux/talkplugin/deb/ trusty main > +#deb http://dl.google.com/linux/talkplugin/deb/ trusty main > +deb http://dl.google.com/linux/talkplugin/deb/ stable main Bye, Tony. -- Dr. A.J.Travis, University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. From tony.travis at abdn.ac.uk Sun Sep 7 11:00:09 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Sun, 7 Sep 2014 16:00:09 +0100 Subject: [Bio-linux-dev] MATE fonts Message-ID: <540C72F9.6050708@abdn.ac.uk> Hi, Tim. I think you've made the MATE fixed-width font a bit too big at 13pt: I've reduced it to 12pt and set only 'slight' hinting, which gives a much better display in my "x2go" client similar to the Unity fonts. Bye, Tony. -- Dr. A.J.Travis, University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. From tony.travis at abdn.ac.uk Wed Sep 10 10:55:27 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Wed, 10 Sep 2014 15:55:27 +0100 Subject: [Bio-linux-dev] Security Message-ID: <5410665F.9040702@abdn.ac.uk> Hi, Tim. I've just noticed that the "guest" account is enabled on Bio-Linux 7 and 8 - Is that by design, or inherited from Ubuntu? I think that's insecure, so I disabled "guest" on the console using: > # disble guest login on console > vim lightdm.conf > ... > [SeatDefaults] > user-session=ubuntu > greeter-session=unity-greeter > autologin-user= > allow-guest=false > ... > service lightdm restart > > # kill any "guest" processes left running > pkill -U guest-BA5aVt Where "guest-BA5aVt" is the obfuscated name of the guest user on that particular system... Bye, Tony. -- Dr. A.J.Travis, University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. From tony.travis at abdn.ac.uk Thu Sep 11 10:52:57 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Thu, 11 Sep 2014 15:52:57 +0100 Subject: [Bio-linux-dev] "bamm" - problems with pthreads Message-ID: <5411B749.20801@abdn.ac.uk> Hi, We're having problems running "bamm" under Bio-Linux 8 / Ubuntu 14.04 LTS. I've compiled the program from source (obtained from GitHub) but when I run it, "bamm" throws an exception. I've tried recompiling using this bug-fix for G++ and tried using "clang" instead, but the problem was not resolved - Any ideas? Thanks, Tony. diff --git a/CMakeLists.txt b/CMakeLists.txt index 9f27da2..10d19ca 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -10,7 +10,7 @@ SET(BAMM_VERSION_DATE 2014-09-05) # Set compiler flags IF(NOT WIN32) SET(CXX_LANGUAGE_FLAGS "-std=c++11") SET(CXX_LANGUAGE_FLAGS "-Wl,--no-as-needed -std=c++11 -pthread") SET(CXX_DEBUG_FLAGS "-g") SET(CXX_WARNING_FLAGS "-Wall -Wextra") SET(CXX_OPTIMIZATION_FLAGS "-O3") soi696 at wildcat:~/Desktop/BAMM2$ bamm -c ControlFileAmoAspeciation.txt BAMM 2.2.0 (2014-09-05) Copyright (C) 2012-2014 Daniel Rabosky BAMM is distributed under the GNU General Public License. See http://bamm-project.org for more information. Random seed: 1410445448 Model type: Speciation/Extinction Reading tree from file . Tree contains 370 taxa. Initial log-likelihood: -1285.74 Reading tree from file . Tree contains 370 taxa. Initial log-likelihood: -1285.74 Reading tree from file . Tree contains 370 taxa. Initial log-likelihood: -1285.74 Reading tree from file . Tree contains 370 taxa. Initial log-likelihood: -1285.74 Running 4 chains for 80000000 generations. terminate called after throwing an instance of 'std::system_error' what(): Enable multithreading to use std::thread: Operation not permitted Aborted -- Dr. A.J.Travis, University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. From tbooth at ceh.ac.uk Fri Sep 12 08:03:53 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Fri, 12 Sep 2014 13:03:53 +0100 Subject: [Bio-linux-dev] Security In-Reply-To: <5410665F.9040702@abdn.ac.uk> References: <5410665F.9040702@abdn.ac.uk> Message-ID: <1410523433.6374.49.camel@balisaur> Hi Tony, For some reason I thought this was an install-time option. Maybe it was in the past or maybe my memory is failing (not for the first time). So yes, it is basically inherited from Ubuntu. But I'm not convinced it is insecure for most users, and certainly if users do want to let their guests on the machine is is more secure then the traditional "here's my password on a post-it note" approach, so I'd be reluctant to remove it without an obvious way to put it back or knowing some specific threat that it exposes. My impression is that only users at the local console can get a guest session, so for servers locked in the server room it should be a moot point? Cheers, TIM On Wed, 2014-09-10 at 15:55 +0100, Tony Travis wrote: > Hi, Tim. > > I've just noticed that the "guest" account is enabled on Bio-Linux 7 and > 8 - Is that by design, or inherited from Ubuntu? > > I think that's insecure, so I disabled "guest" on the console using: > > > # disble guest login on console > > vim lightdm.conf > > ... > > [SeatDefaults] > > user-session=ubuntu > > greeter-session=unity-greeter > > autologin-user= > > allow-guest=false > > ... > > service lightdm restart > > > > # kill any "guest" processes left running > > pkill -U guest-BA5aVt > > Where "guest-BA5aVt" is the obfuscated name of the guest user on that > particular system... > > Bye, > > Tony. > > -- > Dr. A.J.Travis, University of Aberdeen, Institute of Biological and > Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen > AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 > http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis > > > The University of Aberdeen is a charity registered in Scotland, No SC013683. > Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. > _______________________________________________ > Bio-Linux-dev mailing list > Bio-Linux-dev at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 From tbooth at ceh.ac.uk Fri Sep 12 09:35:47 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Fri, 12 Sep 2014 14:35:47 +0100 Subject: [Bio-linux-dev] APT sources in BL 8.0.3 In-Reply-To: <540C5AEB.6020609@abdn.ac.uk> References: <540C586F.8000004@abdn.ac.uk> <540C5AEB.6020609@abdn.ac.uk> Message-ID: <1410528947.6374.68.camel@balisaur> Hi Tony, It looks like some bodged find-and-replace has been run over the contents of sources.list.d/* and you have had to manually fix it. Unfortunately I don't know what has triggered this on your machine because I don't see the problem on mine (test install on bare metal and Packer install on VirtualBox). I suppose I could trigger a patch-up script to be run on first boot, but as usual I'd much rather understand the root cause. Is there anything you did aside from selecting the default options for installation? Cheers, TIM On Sun, 2014-09-07 at 14:17 +0100, Tony Travis wrote: > On 07/09/14 14:06, Tony Travis wrote: > > rdiff -Naur google-talkplugin.list google-talkplugin > > Hi, Tim. > > Sorry, bit of finger trouble there: > > > diff -Naur google-talkplugin.list.orig google-talkplugin.list [ 2:15PM] > > --- google-talkplugin.list.orig 2014-09-02 01:14:20.792528304 +0100 > > +++ google-talkplugin.list 2014-09-07 00:38:08.724681705 +0100 > > @@ -1,3 +1,4 @@ > > ### THIS FILE IS AUTOMATICALLY CONFIGURED ### > > # You may comment out this entry, but any other modifications may be lost. > > -deb http://dl.google.com/linux/talkplugin/deb/ trusty main > > +#deb http://dl.google.com/linux/talkplugin/deb/ trusty main > > +deb http://dl.google.com/linux/talkplugin/deb/ stable main > > Bye, > > Tony. > > -- > Dr. A.J.Travis, University of Aberdeen, Institute of Biological and > Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen > AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 > http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis > > > The University of Aberdeen is a charity registered in Scotland, No SC013683. > Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. > _______________________________________________ > Bio-Linux-dev mailing list > Bio-Linux-dev at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 From tbooth at ceh.ac.uk Fri Sep 12 10:54:20 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Fri, 12 Sep 2014 15:54:20 +0100 Subject: [Bio-linux-dev] Security In-Reply-To: <5412E5C9.3080700@abdn.ac.uk> References: <5410665F.9040702@abdn.ac.uk> <1410523433.6374.49.camel@balisaur> <5412E5C9.3080700@abdn.ac.uk> Message-ID: <1410533660.6374.110.camel@balisaur> Hi Tony, I have never known fail2ban do anything other than lock out legitimate users and generally be a massive PITA. We had something very similar way way back on Bio-Linux 2.1 and we got rid of it sharpish. My preferred option to increase SSH security would be to disable password logins and then make it really really easy (ie. click an icon and follow simple instructions) to generate a public key. The switch to x2go makes this possible as it fully supports key based logins. I'd be interested to hear opinions from others on this list. What do you think? TIM On Fri, 2014-09-12 at 13:23 +0100, Tony Travis wrote: > On 12/09/14 13:03, Tim Booth wrote: > > Hi Tony, > > > > For some reason I thought this was an install-time option. Maybe it was > > in the past or maybe my memory is failing (not for the first time). > > > > So yes, it is basically inherited from Ubuntu. But I'm not convinced it > > is insecure for most users, and certainly if users do want to let their > > guests on the machine is is more secure then the traditional "here's my > > password on a post-it note" approach, so I'd be reluctant to remove it > > without an obvious way to put it back or knowing some specific threat > > that it exposes. My impression is that only users at the local console > > can get a guest session, so for servers locked in the server room it > > should be a moot point? > > Hi, Tim. > > The machine in question was accessed as "guest" from the console in an > unsupervised area (PhD office). However, this machine is also used as a > terminal server. On the question of security, I think it would be wise > to pre-install "fail2ban" for people who enable the SSH server. I think > the Bio-Linux as a terminal server use-case needs to address security. > > Bye, > > Tony. > > -- > Dr. A.J.Travis, University of Aberdeen, Institute of Biological and > Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen > AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 > http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis > > > The University of Aberdeen is a charity registered in Scotland, No SC013683. > Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 From tbooth at ceh.ac.uk Fri Sep 12 12:49:53 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Fri, 12 Sep 2014 17:49:53 +0100 Subject: [Bio-linux-dev] "bamm" - problems with pthreads In-Reply-To: <5411B749.20801@abdn.ac.uk> References: <5411B749.20801@abdn.ac.uk> Message-ID: <1410540593.6374.126.camel@balisaur> Hi Tony, Try this: unzip bamm-2.2.0.zip cd bamm-2.2.0 cmake . make sed 's/$/ -pthread -std=c++11/' CMakeFiles/bamm.dir/link.txt | sh In other words, I think you had the right idea, but CMake defeated you because CMake is a confusing, obfuscating and poorly documented pile of ****. Cheers, TIM On Thu, 2014-09-11 at 15:52 +0100, Tony Travis wrote: > Hi, > > We're having problems running "bamm" under Bio-Linux 8 / Ubuntu 14.04 > LTS. I've compiled the program from source (obtained from GitHub) but > when I run it, "bamm" throws an exception. I've tried recompiling using > this bug-fix for G++ and tried using "clang" instead, but the problem > was not resolved - Any ideas? > > Thanks, > > Tony. > > diff --git a/CMakeLists.txt b/CMakeLists.txt > index 9f27da2..10d19ca 100644 > --- a/CMakeLists.txt > +++ b/CMakeLists.txt > @@ -10,7 +10,7 @@ SET(BAMM_VERSION_DATE 2014-09-05) > > # Set compiler flags > IF(NOT WIN32) > > SET(CXX_LANGUAGE_FLAGS "-std=c++11") > SET(CXX_LANGUAGE_FLAGS "-Wl,--no-as-needed -std=c++11 -pthread") > SET(CXX_DEBUG_FLAGS "-g") SET(CXX_WARNING_FLAGS "-Wall -Wextra") > SET(CXX_OPTIMIZATION_FLAGS "-O3") > > soi696 at wildcat:~/Desktop/BAMM2$ bamm -c ControlFileAmoAspeciation.txt > BAMM 2.2.0 (2014-09-05) > Copyright (C) 2012-2014 Daniel Rabosky > BAMM is distributed under the GNU General Public License. > See http://bamm-project.org for more information. > > Random seed: 1410445448 > > Model type: Speciation/Extinction > > Reading tree from file . > Tree contains 370 taxa. > > Initial log-likelihood: -1285.74 > > Reading tree from file . > Tree contains 370 taxa. > > Initial log-likelihood: -1285.74 > > Reading tree from file . > Tree contains 370 taxa. > > Initial log-likelihood: -1285.74 > > Reading tree from file . > Tree contains 370 taxa. > > Initial log-likelihood: -1285.74 > > Running 4 chains for 80000000 generations. > > terminate called after throwing an instance of 'std::system_error' > what(): Enable multithreading to use std::thread: Operation not permitted > Aborted > > -- > Dr. A.J.Travis, University of Aberdeen, Institute of Biological and > Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen > AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 > http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis > > > The University of Aberdeen is a charity registered in Scotland, No SC013683. > Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. > _______________________________________________ > Bio-Linux-dev mailing list > Bio-Linux-dev at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 From tony.travis at abdn.ac.uk Fri Sep 12 17:21:01 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Fri, 12 Sep 2014 22:21:01 +0100 Subject: [Bio-linux-dev] APT sources in BL 8.0.3 In-Reply-To: <1410528947.6374.68.camel@balisaur> References: <540C586F.8000004@abdn.ac.uk> <540C5AEB.6020609@abdn.ac.uk> <1410528947.6374.68.camel@balisaur> Message-ID: <541363BD.30602@abdn.ac.uk> On 12/09/14 14:35, Tim Booth wrote: > Hi Tony, > > It looks like some bodged find-and-replace has been run over the > contents of sources.list.d/* and you have had to manually fix it. > Unfortunately I don't know what has triggered this on your machine > because I don't see the problem on mine (test install on bare metal and > Packer install on VirtualBox). Hi, Tim. Actually, it was a clean install from your 8.0.3 .iso, not an upgrade. > I suppose I could trigger a patch-up script to be run on first boot, but > as usual I'd much rather understand the root cause. Is there anything > you did aside from selecting the default options for installation? No, this one was to an Adaptec hardware RAID6 (i.e. not my usual md RAID6). I did partition the disk manually in the installer and preserved /home, but that's all - Otherwise, completely default. I only noticed the problem when doing an update after the installation and first boot from the installed system. I'm going to do another install on an identical machine, and I'll let you know if I get the same problem on that one. Bye, Tony. -- Dr. A.J.Travis, University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. From tony.travis at abdn.ac.uk Fri Sep 12 17:36:34 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Fri, 12 Sep 2014 22:36:34 +0100 Subject: [Bio-linux-dev] "bamm" - problems with pthreads In-Reply-To: <1410540593.6374.126.camel@balisaur> References: <5411B749.20801@abdn.ac.uk> <1410540593.6374.126.camel@balisaur> Message-ID: <54136762.4030900@abdn.ac.uk> On 12/09/14 17:49, Tim Booth wrote: > Hi Tony, > > Try this: > > unzip bamm-2.2.0.zip > cd bamm-2.2.0 > cmake . > make > sed 's/$/ -pthread -std=c++11/' CMakeFiles/bamm.dir/link.txt | sh > > In other words, I think you had the right idea, but CMake defeated you > because CMake is a confusing, obfuscating and poorly documented pile of > ****. Hi, Tim. Got to agree with you there: https://github.com/macroevolution/bamm/issues/132 Got a working version now :-) Thanks, Tony. -- Dr. A.J.Travis, University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683.